CALEXICO, Calif. — For generations, residents of the Southern California border town of Calexico watched with trepidation as their river turned into a cesspool, contaminated by the booming human and industrial development on the other side of the border in Mexico.

Noxious sewage filled with feces, industrial chemicals and other raw waste regularly comes in through the New River, which flows from Mexico’s Mexicali Valley and through Calexico, leaving neighborhoods along the waterway engulfed in pungent fumes. And it’s not just the river: From above, smoke billows from Mexican factories, illicit medical burn sites and tire pits, fueling widespread asthma in the region.

As Washington debates spending billions to shore up barriers along the 2,000-mile southwest border, many residents in California’s Imperial Valley feel at least some of that money could be spent to address the region’s public health threats. Just feet away from Calexico, Mexico’s lax environmental rules and enforcement pose a regular menace.

“It’s a pit of infection,” said Arturo Santiago, 50, who lives in a neighborhood adjacent to the river in west Calexico, atop a steep overlook. “It smells like farts if you open your window.”

Mexico has long treated the New River as a drain rather than a river, discharging raw, untreated sewage from Mexicali homes and businesses directly into the water. The explosive growth of Mexicali into a city of a million people in recent decades, in part accelerated by the North American Free Trade Agreement, has exacerbated the problem.

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Debris left by the river. Efforts to clean up the pollution and waste on the American side have faced long delays.CreditEmily Kask for The New York Times

Today, even after various cleanup efforts, large mounds of unnatural foam and piles of trash — illegally dumped — float atop the dark green stream, which flows into the United States through a hole in a slatted border fence and flows north toward the Salton Sea in California.

A 2018 report published by the regional water board shows that the river, where it crosses the border, contains extreme fecal coliform and E. coli concentrations that are orders of magnitude beyond established targets, because of the tens of millions of gallons of raw sewage that have been dumped into the river in recent years.

State lawmakers have noted that the river is believed to carry pathogens that cause tuberculosis, encephalitis, polio, cholera, hepatitis, and typhoid. But Calexico, a small town of 40,000 in California’s Imperial Valley farm belt, has had little recourse but to endure the public health risks.

Miguel Figueroa, Calexico’s assistant city manager, called the river a “historic environmental justice problem.” The westside homes adjacent to the river have historically been occupied by low-income residents, many of whom work in agriculture. Their relative poverty, plus the Imperial Valley’s lack of political clout in Sacramento, he said, were significant obstacles to drawing sustained attention to the river.

Many have called for enclosing the river and diverting its waters to filter out pollutants.

Those living near the river are not the only ones with concerns. The river also poses a security issue for border agents, said David Kim, a spokesman for Customs and Border Protection. “Smuggling organizations still use the New River to move humans into the U.S.,” said Mr. Kim, noting that border agents are unable to go into the water to chase border violators because it is too hazardous.

The air pollution concerns also have been worrying. Gilbert Rebollar, a board member of the Brawley Elementary School District, to the north of Calexico, said students regularly cannot go outside because the air quality is too dangerous. About 20 percent of children in Imperial County have asthma, according to a 2016 California Health Interview Survey, roughly twice the state average. That number may be higher in towns directly adjacent to the border.

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State lawmakers have noted that the river is believed to carry pathogens that cause tuberculosis, encephalitis, polio, cholera, hepatitis, and typhoid.CreditEmily Kask for The New York Times

“There is a crisis here but it has nothing to do with immigration,” said Mr. Rebollar, who is also an analyst at the Imperial County Air Pollution Control District. “And it’s not just about money. It’s about holding Mexico accountable. Some of these hospitals are going out at night and burning medical waste.”

Mr. Santiago, like many people living in the neighborhoods overlooking the river, said he had gone through about four air-conditioning units since he moved into his house in 2000. He and his neighbors suspect the corrosion damage is caused by chemicals in the air, though the local air pollution control board said it was not aware of these complaints.

Rebeca and Miguel Zapata, whose grandson, Kevin, 15, often visits and has severe asthma, said they moved to the neighborhood adjacent to the river in the 1990s because the homes were cheaper there. Ms. Zapata, 76, said her allergies have become so severe she has to go to the doctor weekly for treatment.

Public health officials in the region said allergies are difficult to pin to specific environmental causes. But fears and suspicions in the community persist.

Nearly 20 years ago, the Environmental Protection Agency granted $31 million to pay for sanitation projects on the Mexican side of the border, completed in 2007, to improve the water quality before it reached the United States. That project, funded by North American Development Bank, which was created by Nafta, encased the river on the Mexican side in piping. No such piping was installed on the American side.

But by May 2017, the regional California Water Quality Control Board was raising fresh alarms. In spite of progress, “the deteriorating condition of the sewage infrastructure” built in Mexico posed a severe threat to the water quality, the board wrote in a resolution addressed to several federal and international agencies. At least once a month, for at least six months, one million to 13 million gallons of raw sewage were released into the river by Mexicali, the water board said.

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Many have called for enclosing the river and diverting its waters to filter out pollutants.CreditEmily Kask for The New York Times

Many along the border have groused about funding for water treatment projects not going to the American side.

“It’s been really hard to digest and understand that American resources are going into Mexico,” said Mr. Figueroa, the assistant city manager. “It’s shameful, because the last time we checked Imperial County is in the state of California.”

Community efforts to redevelop the river on the American side have faced delays over 15 years. About two dozens stakeholders at the local, state, and federal level have some oversight responsibility for the New River. The bureaucratic glut is perhaps partly to blame for the delays.

“For crying out loud, when you have environmental problems that are that prevalent, that are affecting human beings and human health, that should be at the very top of the list,” said Eduardo Garcia, a Democratic member of the State Assembly who has sought to bring attention to the problem in the State Legislature.

Two crucial developments have revived the cleanup efforts. In 2016 the state allocated $1.4 million to draft an engineering plan to begin collecting and treating the water. Then, in 2018, a state proposition allocated $10 million toward the project, part of a broader package to rehabilitate the Salton Sea.

Mr. Figueroa is hopeful that, with enough money now to get the project off the ground, local officials can use the momentum to find the additional $10 million to $20 million they need to complete the project.

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Many along the border have groused about funding for water treatment projects not going to the American side.CreditEmily Kask for The New York Times

“For the longest time we heard that we needed a shovel-ready project. And guess what, we have a shovel-ready project now and we have partial funding,” he said.

There has been more success and investment in combating the air quality problems. The California Environmental Protection Agency said it maintains strong relationships with its Mexican counterparts. Federal money, meanwhile, has bolstered air-quality monitoring programs in Mexicali, which help Mexican authorities crack down on illegal trash-burning.

Jared Blumenfeld, the new secretary of the California Environmental Protection Agency under Gov. Gavin Newsom, said the state was “committed to doing the project” on the New River. He shared a video from a visit to Mexicali in 2011 that showed blood draining into the river from a slaughterhouse.

Mr. Blumenfeld said he would be “fairly shocked” if money for the New River were not included on a new list of federal funding priorities. “We as a country have not made good on our commitments under Nafta to continue to make border improvements, and the New River is so emblematic of this,” he said.

Residents here, after decades of promises, are not so sure that help will arrive, and are suspicious of officials at every level of government.

“They’re either stealing the money or they’re not getting any,” said Mr. Santiago. “But they don’t pay attention. They don’t pay attention.”

A version of this article appears in print on , on Page A14 of the New York edition with the headline: A California Border Town Swept Up in Mexico’s Waste. Order Reprints | Today’s Paper | Subscribe